I managed to add the opening video using Terminal rather than SSH.
I copied the relevant files to an easily accessible location and then used the mv command.

(Please only do this at your own risk, I will not be to blame for any bricked devices!)

eg.

to backup the original file,
cp /etc/hildon-welcome.d/*.conf /home/user/MyDocs/

then to put in the video file (any way to optify this?)
mv /home/user/MyDocs/Matrix/media/*.avi /usr/share/hildon-welcome/media/

and to copy over the file that tells the phone which movie to play:
mv /home/user/MyDocs/Matrix/conf/*.conf /etc/hildon-welcome.d/

Nice work on the video.